Fluorine in PDB 3o0u: Cathepsin K Covalently Bound to A Cyano-Pyrimidine Inhibitor with Improved Selectivity Over Herg

All present enzymatic activity of Cathepsin K Covalently Bound to A Cyano-Pyrimidine Inhibitor with Improved Selectivity Over Herg:
3.4.22.38;

The structure of Cathepsin K Covalently Bound to A Cyano-Pyrimidine Inhibitor with Improved Selectivity Over Herg, PDB code: 3o0u was solved by X.Fradera, M.Van Zeeland, J.C.M.Uitdehaag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.99 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.695, 48.967, 103.958, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 21.7

The binding sites of Fluorine atom in the Cathepsin K Covalently Bound to A Cyano-Pyrimidine Inhibitor with Improved Selectivity Over Herg (pdb code 3o0u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cathepsin K Covalently Bound to A Cyano-Pyrimidine Inhibitor with Improved Selectivity Over Herg, PDB code: 3o0u:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cathepsin K Covalently Bound to A Cyano-Pyrimidine Inhibitor with Improved Selectivity Over Herg


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cathepsin K Covalently Bound to A Cyano-Pyrimidine Inhibitor with Improved Selectivity Over Herg within 5.0Å range: probe atom residue distance (Å) B Occ A:F216 b:29.8 occ:1.00 F8 A:O47216 0.0 29.8 1.0 C7 A:O47216 1.3 24.9 1.0 F9 A:O47216 2.1 28.9 1.0 F10 A:O47216 2.1 29.9 1.0 C1 A:O47216 2.3 23.5 1.0 C2 A:O47216 2.8 23.1 1.0 CD2 A:TYR67 3.2 16.3 1.0 O A:GLY66 3.3 13.5 1.0 C6 A:O47216 3.4 21.6 1.0 CE2 A:TYR67 3.4 16.4 1.0 CD2 A:LEU209 3.7 14.8 1.0 C3 A:O47216 4.1 22.3 1.0 CA A:TYR67 4.1 13.2 1.0 CG A:TYR67 4.2 15.1 1.0 C A:GLY66 4.2 13.4 1.0 CB A:ALA134 4.3 9.2 1.0 SD A:MET68 4.3 14.7 1.0 C5 A:O47216 4.5 22.2 1.0 N A:TYR67 4.6 13.5 1.0 CZ A:TYR67 4.6 16.6 1.0 CB A:TYR67 4.6 14.2 1.0 C4 A:O47216 4.8 23.8 1.0 O A:HOH236 4.8 10.3 1.0

Fluorine binding site 2 out of 3 in the Cathepsin K Covalently Bound to A Cyano-Pyrimidine Inhibitor with Improved Selectivity Over Herg


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cathepsin K Covalently Bound to A Cyano-Pyrimidine Inhibitor with Improved Selectivity Over Herg within 5.0Å range: probe atom residue distance (Å) B Occ A:F216 b:28.9 occ:1.00 F9 A:O47216 0.0 28.9 1.0 C7 A:O47216 1.3 24.9 1.0 F8 A:O47216 2.1 29.8 1.0 F10 A:O47216 2.1 29.9 1.0 C1 A:O47216 2.3 23.5 1.0 C2 A:O47216 2.9 23.1 1.0 CB A:ALA134 3.4 9.2 1.0 CB A:LEU160 3.4 16.2 1.0 C6 A:O47216 3.5 21.6 1.0 O A:LEU160 3.8 16.3 1.0 CD2 A:LEU209 3.8 14.8 1.0 C A:LEU160 4.0 16.0 1.0 C3 A:O47216 4.2 22.3 1.0 CE2 A:TYR67 4.3 16.4 1.0 CA A:LEU160 4.3 16.7 1.0 CD1 A:LEU160 4.4 15.9 1.0 N A:ASN161 4.5 15.2 1.0 CG A:LEU160 4.5 15.4 1.0 CD2 A:TYR67 4.6 16.3 1.0 C5 A:O47216 4.6 22.2 1.0 CA A:ALA134 4.7 10.7 1.0 O A:HIS162 4.7 13.7 1.0 N A:HIS162 4.9 13.4 1.0 C4 A:O47216 4.9 23.8 1.0

Fluorine binding site 3 out of 3 in the Cathepsin K Covalently Bound to A Cyano-Pyrimidine Inhibitor with Improved Selectivity Over Herg


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cathepsin K Covalently Bound to A Cyano-Pyrimidine Inhibitor with Improved Selectivity Over Herg within 5.0Å range: probe atom residue distance (Å) B Occ A:F216 b:29.9 occ:1.00 F10 A:O47216 0.0 29.9 1.0 C7 A:O47216 1.3 24.9 1.0 F8 A:O47216 2.1 29.8 1.0 F9 A:O47216 2.1 28.9 1.0 C1 A:O47216 2.4 23.5 1.0 C6 A:O47216 2.8 21.6 1.0 CB A:ALA134 3.4 9.2 1.0 O A:HIS162 3.5 13.7 1.0 C2 A:O47216 3.6 23.1 1.0 CB A:ALA163 3.7 11.6 1.0 C A:HIS162 3.7 13.0 1.0 N A:ALA163 4.0 11.7 1.0 CA A:ALA163 4.1 11.8 1.0 N A:HIS162 4.2 13.4 1.0 CA A:ALA134 4.2 10.7 1.0 C5 A:O47216 4.2 22.2 1.0 O A:GLY66 4.3 13.5 1.0 SD A:MET68 4.3 14.7 1.0 CA A:HIS162 4.4 13.1 1.0 C3 A:O47216 4.8 22.3 1.0 CE A:MET68 4.8 11.3 1.0 C A:ASN161 4.8 14.0 1.0 CD2 A:LEU209 5.0 14.8 1.0

Z.Rankovic, J.Cai, J.Kerr, X.Fradera, J.Robinson, A.Mistry, W.Finlay, G.Mcgarry, F.Andrews, W.Caulfield, I.Cumming, M.Dempster, J.Waller, W.Arbuckle, M.Anderson, I.Martin, A.Mitchell, C.Long, M.Baugh, P.Westwood, E.Kinghorn, P.Jones, J.C.Uitdehaag, M.Van Zeeland, D.Potin, L.Saniere, A.Fouquet, F.Chevallier, H.Deronzier, C.Dorleans, E.Nicolai. Optimisation of 2-Cyano-Pyrimidine Inhibitors of Cathepsin K: Improving Selectivity Over Herg. Bioorg.Med.Chem.Lett. V. 20 6237 2010.
ISSN: ISSN 0960-894X
PubMed: 20843687
DOI: 10.1016/J.BMCL.2010.08.101